Optimization of a protein's pharmaceutical properties is usually carried out by rational design and/or directed evolution. Here we test an alternative approach based on ancestral sequence reconstruction. Using available genomic sequence data on coagulation factor VIII and predictive models of molecular evolution, we engineer protein variants with improved activity, stability, and biosynthesis potential and reduced inhibition by anti-drug antibodies. In principle, this approach can be applied to any protein drug based on a conserved gene sequence.
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Doering, C.B. et al. Thromb. Haemost. 88, 450–458 (2002).
Doering, C.B., Healey, J.F., Parker, E.T., Barrow, R.T. & Lollar, P. J. Biol. Chem. 277, 38345–38349 (2002).
Zakas, P.M. et al. PLoS One 7, e49481 (2012).
Zakas, P.M., Vanijcharoenkarn, K., Markovitz, R.C., Meeks, S.L. & Doering, C.B. J. Thromb. Haemost. 13, 72–81 (2015).
Sabatino, D.E. et al. Blood 114, 4562–4565 (2009).
Doering, C.B., Healey, J.F., Parker, E.T., Barrow, R.T. & Lollar, P. J. Biol. Chem. 279, 6546–6552 (2004).
Parker, E.T., Doering, C.B. & Lollar, P. J. Biol. Chem. 281, 13922–13930 (2006).
Zuckerkandl, E. & Pauling, L. J. Theor. Biol. 8, 357–366 (1965).
Merkl, R. & Sterner, R. Biol. Chem. 397, 1–21 (2016).
Risso, V.A., Gavira, J.A., Mejia-Carmona, D.F., Gaucher, E.A. & Sanchez-Ruiz, J.M. J. Am. Chem. Soc. 135, 2899–2902 (2013).
Ivarsson, Y., Mackey, A.J., Edalat, M., Pearson, W.R. & Mannervik, B. J. Biol. Chem. 278, 8733–8738 (2003).
Harms, M.J. et al. Proc. Natl. Acad. Sci. USA 110, 11475–11480 (2013).
Kratzer, J.T. et al. Proc. Natl. Acad. Sci. USA 111, 3763–3768 (2014).
Wilson, C. et al. Science 347, 882–886 (2015).
Gaucher, E.A., Govindarajan, S. & Ganesh, O.K. Nature 451, 704–707 (2008).
Brown, H.C., Gangadharan, B. & Doering, C.B. J. Biol. Chem. 286, 24451–24457 (2011).
Pipe, S.W., Eickhorst, A.N., McKinley, S.H., Saenko, E.L. & Kaufman, R.J. Blood 93, 176–183 (1999).
Leong, L. et al. Blood 125, 392–398 (2015).
Markovitz, R.C., Healey, J.F., Parker, E.T., Meeks, S.L. & Lollar, P. Blood 121, 2785–2795 (2013).
Esmon, C.T. & Lollar, P. J. Biol. Chem. 271, 13882–13887 (1996).
Barrow, R.T., Parker, E.T., Krishnaswamy, S. & Lollar, P. J. Biol. Chem. 269, 26796–26800 (1994).
Healey, J.F. et al. J. Thromb. Haemost. 5, 512–519 (2007).
Meeks, S.L., Healey, J.F., Parker, E.T., Barrow, R.T. & Lollar, P. Blood 110, 4234–4242 (2007).
Bi, L. et al. Nat. Genet. 10, 119–121 (1995).
Brown, H.C. et al. Mol. Ther. Methods Clin. Dev. 1, 14036 (2014).
Gaucher, E.A., Thomson, J.M., Burgan, M.F. & Benner, S.A. Nature 425, 285–288 (2003).
Huelsenbeck, J.P., Ronquist, F., Nielsen, R. & Bollback, J.P. Science 294, 2310–2314 (2001).
Yang, Z. Mol. Biol. Evol. 24, 1586–1591 (2007).
Lollar, P., Parker, E.T. & Fay, P.J. J. Biol. Chem. 267, 23652–23657 (1992).
Healey, J.F. et al. Thromb. Haemost. 102, 35–41 (2009).
Barrow, R.T. & Lollar, P. J. Thromb. Haemost. 4, 2223–2229 (2006).
Larsen, J.E., Lund, O. & Nielsen, M. Immunome Res. 2, 2 (2006).
Spencer, H.T. et al. Mol. Ther. 19, 302–309 (2011).
Parker, E.T. & Lollar, P. Thromb. Haemost. 89, 480–485 (2003).
Dixon, W.J. Neurosci. Biobehav. Rev. 15, 47–50 (1991).
McIntosh, J. et al. Blood 121, 3335–3344 (2013).
This work was supported by funding from the National Institutes of Health/National Heart, Lung, and Blood Institute for the Translational Research Centers in Thrombotic and Hemostatic Disorders (U54 HL112309 to H.T.S., S.L.M., and C.B.D.), the Bayer Hemophilia Awards Program, Bayer HealthCare (C.B.D.) as well as a research partnership between Children's Healthcare of Atlanta and the Georgia Institute of Technology (C.B.D. and E.A.G.). We also thank E.T. Parker (Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University, Atlanta, Georgia, USA) for technical assistance with the in vivo mouse studies.
C.B.D., E.A.G., H.T.S. and P.M.Z. are inventors on a patent application describing ancestral FVIII technology filed by Emory University/Children's Healthcare of Atlanta and the Georgia Institute of Technology. C.B.D. and H.T.S. are co-founders of Expression Therapeutics, LLC, and own equity in the company. Expression Therapeutics owns the intellectual property associated with ET3 and has plans to commercially develop technology used in the research described in this paper. The terms of this arrangement have been reviewed and approved by Emory University in accordance with its conflict of interest policies.
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Zakas, P., Brown, H., Knight, K. et al. Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction. Nat Biotechnol 35, 35–37 (2017). https://doi.org/10.1038/nbt.3677
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